/* Routines for getting variables passed in from web page
 * forms via CGI.
 *
 * This file is copyright 2002 Jim Kent, but license is hereby
 * granted for all use - public, private or commercial. */

#include "common.h"
#include "hash.h"
#include "cheapcgi.h"
#include "portable.h"
#include "linefile.h"
#include "errabort.h"
#ifndef GBROWSE
#include "mime.h"
#endif /* GBROWSE */
#include <signal.h>

/* These three variables hold the parsed version of cgi variables. */
static char *inputString = NULL;
static unsigned long inputSize;
static struct hash *inputHash = NULL;
static struct cgiVar *inputList = NULL;

static boolean haveCookiesHash = FALSE;
static struct hash *cookieHash = NULL;
static struct cgiVar *cookieList = NULL;

/* should cheapcgi use temp files to store uploaded files */
static boolean doUseTempFile = FALSE;

void dumpCookieList()
/* Print out the cookie list. */
{
  struct cgiVar *v;
  for (v = cookieList; v != NULL; v = v->next)
    printf("%s=%s (%d)\n", v->name, v->val, v->saved);
}

void useTempFile()
/* tell cheapcgi to use temp files */
{
  doUseTempFile = TRUE;
}

boolean cgiIsOnWeb()
/* Return TRUE if looks like we're being run as a CGI. */
{
  return getenv("REQUEST_METHOD") != NULL;
}

char *cgiRequestMethod()
/* Return CGI REQUEST_METHOD (such as 'GET/POST/PUT/DELETE/HEAD') */
{
  return getenv("REQUEST_METHOD");
}

char *cgiRequestUri()
/* Return CGI REQUEST_URI */
{
  return getenv("REQUEST_URI");
}

char *cgiRequestContentLength()
/* Return HTTP REQUEST CONTENT_LENGTH if available*/
{
  return getenv("CONTENT_LENGTH");
}

char *cgiScriptName()
/* Return name of script so libs can do context-sensitive stuff. */
{
  return getenv("SCRIPT_NAME");
}

char *cgiServerName()
/* Return name of server, better to use cgiServerNamePort() for
   actual URL construction */
{
  return getenv("SERVER_NAME");
}

char *cgiServerPort()
/* Return port number of server, default 80 if not found */
{
  char *port = getenv("SERVER_PORT");
  if (port)
    return port;
  else
    return "80";
}

char *cgiServerNamePort()
/* Return name of server with port if different than 80 */
{
  char *port = cgiServerPort();
  char *namePort = cgiServerName();
  struct dyString *result = newDyString(256);
  if (namePort) {
    dyStringPrintf(result, "%s", namePort);
    if (differentString(port, "80"))
      dyStringPrintf(result, ":%s", port);
    return dyStringCannibalize(&result);
  } else
    return NULL;
}

char *cgiRemoteAddr()
/* Return IP address of client (or "unknown"). */
{
  static char *dunno = "unknown";
  char *remoteAddr = getenv("REMOTE_ADDR");
  if (remoteAddr == NULL)
    remoteAddr = dunno;
  return remoteAddr;
}

char *cgiUserAgent()
/* Return remote user agent (HTTP_USER_AGENT) or NULL if remote user agent is
   not known */
{
  return getenv("HTTP_USER_AGENT");
}

enum browserType cgiClientBrowser(char **browserQualifier,
                                  enum osType *clientOs,
                                  char **clientOsQualifier)
/* Return client browser type determined from (HTTP_USER_AGENT)
   Optionally requuest the additional info about the client */
{
  // WARNING: The specifics of the HTTP_USER_AGENT vary widely.
  //          This has only been tested on a few cases.
  static enum browserType clientBrowser = btUnknown;
  static enum browserType clientOsType = osUnknown;
  static char *clientBrowserExtra = NULL;
  static char *clientOsExtra = NULL;

  if (clientBrowser == btUnknown) {
    char *userAgent = cgiUserAgent();
    if (userAgent != NULL) {
      // warn(userAgent);  // Use this to investigate other cases
      char *ptr = NULL;

      // Determine the browser
      if ((ptr = stringIn("Opera", userAgent)) != NULL) // Must be before IE
      {
        clientBrowser = btOpera;
      } else if ((ptr = stringIn("MSIE ", userAgent)) != NULL) {
        clientBrowser = btIE;
        ptr += strlen("MSIE ");
        clientBrowserExtra = cloneFirstWordByDelimiter(ptr, ';');
      } else if ((ptr = stringIn("Firefox", userAgent)) != NULL) {
        clientBrowser = btFF;
        ptr += strlen("(Firefox/");
        clientBrowserExtra = cloneFirstWordByDelimiter(ptr, ' ');
      } else if ((ptr = stringIn("Chrome", userAgent)) !=
                 NULL) // Must be before Safari
      {
        clientBrowser = btChrome;
        ptr += strlen("Chrome/");
        clientBrowserExtra = cloneFirstWordByDelimiter(ptr, ' ');
      } else if ((ptr = stringIn("Safari", userAgent)) != NULL) {
        clientBrowser = btSafari;
        ptr += strlen("Safari/");
        clientBrowserExtra = cloneFirstWordByDelimiter(ptr, ' ');
      } else {
        clientBrowser = btOther;
      }

      // Determine the OS
      if ((ptr = stringIn("Windows", userAgent)) != NULL) {
        clientOsType = osWindows;
        ptr += strlen("Windows ");
        clientOsExtra = cloneFirstWordByDelimiter(ptr, ';');
      } else if ((ptr = stringIn("Linux", userAgent)) != NULL) {
        clientOsType = osLinux;
        ptr += strlen("Linux ");
        clientOsExtra = cloneFirstWordByDelimiter(ptr, ';');
      } else if ((ptr = stringIn("Mac ", userAgent)) != NULL) {
        clientOsType = osMac;
        ptr += strlen("Mac ");
        clientOsExtra = cloneFirstWordByDelimiter(ptr, ';');
      } else {
        clientOsType = osOther;
      }
    }
  }
  if (browserQualifier != NULL) {
    if (clientBrowserExtra != NULL)
      *browserQualifier = cloneString(clientBrowserExtra);
    else
      *browserQualifier = NULL;
  }
  if (clientOs != NULL)
    *clientOs = clientOsType;
  if (clientOsQualifier != NULL) {
    if (clientOsExtra != NULL)
      *clientOsQualifier = cloneString(clientOsExtra);
    else
      *clientOsQualifier = NULL;
  }

  return clientBrowser;
}

char *_cgiRawInput()
/* For debugging get the unprocessed input. */
{
  return inputString;
}

static void getQueryInputExt(boolean abortOnErr)
/* Get query string from environment if they've used GET method. */
{
  inputString = getenv("QUERY_STRING");
  if (inputString == NULL) {
    if (abortOnErr)
      errAbort("No QUERY_STRING in environment.");
    inputString = cloneString("");
    return;
  }
  inputString = cloneString(inputString);
}

static void getQueryInput()
/* Get query string from environment if they've used GET method. */
{
  getQueryInputExt(TRUE);
}

static void getPostInput()
/* Get input from file if they've used POST method.
 * Grab any GET QUERY_STRING input first. */
{
  char *s;
  long i;
  int r;

  getQueryInputExt(FALSE);
  int getSize = strlen(inputString);

  s = getenv("CONTENT_LENGTH");
  if (s == NULL)
    errAbort("No CONTENT_LENGTH in environment.");
  if (sscanf(s, "%lu", &inputSize) != 1)
    errAbort("CONTENT_LENGTH isn't a number.");
  s = getenv("CONTENT_TYPE");
  if (s != NULL && startsWith("multipart/form-data", s)) {
    /* use MIME parse on input stream instead, can handle large uploads */
    /* inputString must not be NULL so it knows it was set */
    return;
  }
  int len = getSize + inputSize;
  if (getSize > 0)
    ++len;
  char *temp = needMem((size_t)len + 1);
  for (i = 0; i < inputSize; ++i) {
    r = getc(stdin);
    if (r == EOF)
      errAbort("Short POST input.");
    temp[i] = r;
  }
  if (getSize > 0)
    temp[i++] = '&';
  strncpy(temp + i, inputString, getSize);
  temp[len] = 0;
  freeMem(inputString);
  inputString = temp;
}

#define memmem(hay, haySize, needle, needleSize)                               \
  memMatch(needle, needleSize, hay, haySize)

#ifndef GBROWSE
static void cgiParseMultipart(struct hash **retHash, struct cgiVar **retList)
/* process a multipart form */
{
  char h[1024]; /* hold mime header line */
  char *s = NULL, *ct = NULL;
  struct dyString *dy = newDyString(256);
  struct mimeBuf *mb = NULL;
  struct mimePart *mp = NULL;
  char **env = NULL;
  struct hash *hash = newHash(6);
  struct cgiVar *list = NULL, *el;
  extern char **environ;

  // debug
  // fprintf(stderr,"GALT: top of cgiParseMultipart()\n");
  // fflush(stderr);

  /* find the CONTENT_ environment strings, use to make Alternate Header string
   * for MIME */
  for (env = environ; *env; env++)
    if (startsWith("CONTENT_", *env)) {
      // debug
      // fprintf(stderr,"%s\n",*env);  //debug
      safef(h, sizeof(h), "%s", *env);
      s = strchr(
          h, '_'); /* change env syntax to MIME style header, from _= to -: */
      if (!s)
        errAbort("expecting '_' parsing env var %s for MIME alt header", *env);
      *s = '-';
      s = strchr(h, '=');
      if (!s)
        errAbort("expecting '=' parsing env var %s for MIME alt header", *env);
      *s = ':';
      dyStringPrintf(dy, "%s\r\n", h);
    }
  dyStringAppend(dy, "\r\n"); /* blank line at end means end of headers */

  // debug
  // fprintf(stderr,"Alternate Header Text:\n%s",dy->string);
  // fflush(stderr);
  mb = initMimeBuf(STDIN_FILENO);
  // debug
  // fprintf(stderr,"got past initMimeBuf(STDIN_FILENO)\n");
  // fflush(stderr);
  mp = parseMultiParts(
      mb, cloneString(dy->string)); /* The Alternate Header will get freed */
  freeDyString(&dy);
  if (!mp->multi) /* expecting multipart child parts */
    errAbort("Malformatted multipart-form.");

  // debug
  // fprintf(stderr,"GALT: Wow got past parse of MIME!\n");
  // fflush(stderr);

  ct = hashFindVal(mp->hdr, "content-type");
  // debug
  // fprintf(stderr,"GALT: main content-type: %s\n",ct);
  // fflush(stderr);
  if (!startsWith("multipart/form-data", ct))
    errAbort("main content-type expected starts with [multipart/form-data], "
             "found [%s]",
             ct);

  for (mp = mp->multi; mp; mp = mp->next) {
    char *cd = NULL, *cdMain = NULL, *cdName = NULL, *cdFileName = NULL,
         *ct = NULL;
    cd = hashFindVal(mp->hdr, "content-disposition");
    ct = hashFindVal(mp->hdr, "content-type");
    // debug
    // fprintf(stderr,"GALT: content-disposition: %s\n",cd);
    // fprintf(stderr,"GALT: content-type: %s\n",ct);
    // fflush(stderr);
    cdMain = getMimeHeaderMainVal(cd);
    cdName = getMimeHeaderFieldVal(cd, "name");
    cdFileName = getMimeHeaderFieldVal(cd, "filename");
    // debug
    // fprintf(stderr,"cgiParseMultipart: main:[%s], name:[%s],
    // filename:[%s]\n",cdMain,cdName,cdFileName);
    // fflush(stderr);
    if (!sameString(cdMain, "form-data"))
      errAbort("main content-type expected [form-data], found [%s]", cdMain);

    // debug
    // fprintf(stderr,"GALT: mp->size[%llu], mp->binary=[%d], mp->fileName=[%s],
    // mp=>data:[%s]\n",
    //(unsigned long long) mp->size, mp->binary, mp->fileName,
    // mp->binary && mp->data ? "<binary data not safe to print>" : mp->data);
    // fflush(stderr);

    /* filename if there is one */
    /* Internet Explorer on Windows is sending full path names, strip
     * directory name from those.  Using \ and / and : as potential
     * path separator characters, e.g.:
     *	 C:\Documents and Settings\tmp\file.txt.gz
     */
    if (cdFileName) {
      char *lastPathSep = strrchr(cdFileName, (int)'\\');
      if (!lastPathSep)
        lastPathSep = strrchr(cdFileName, (int)'/');
      if (!lastPathSep)
        lastPathSep = strrchr(cdFileName, (int)':');
      char varNameFilename[256];
      safef(varNameFilename, sizeof(varNameFilename), "%s__filename", cdName);
      AllocVar(el);
      if (lastPathSep)
        el->val = cloneString(lastPathSep + 1);
      else
        el->val = cloneString(cdFileName);
      slAddHead(&list, el);
      hashAddSaveName(hash, varNameFilename, el, &el->name);
    }

    if (mp->data) {
      if (mp->binary) {
        char varNameBinary[256];
        char addrSizeBuf[40];
        safef(varNameBinary, sizeof(varNameBinary), "%s__binary", cdName);
        safef(addrSizeBuf, sizeof(addrSizeBuf), "%lu %llu",
              (unsigned long)mp->data, (unsigned long long)mp->size);
        AllocVar(el);
        el->val = cloneString(addrSizeBuf);
        slAddHead(&list, el);
        hashAddSaveName(hash, varNameBinary, el, &el->name);
      } else /* normal variable, not too big, does not contain zeros */
      {
        AllocVar(el);
        el->val = mp->data;
        slAddHead(&list, el);
        hashAddSaveName(hash, cdName, el, &el->name);
      }
    } else if (mp->fileName) {
      char varNameData[256];
      safef(varNameData, sizeof(varNameData), "%s__data", cdName);
      AllocVar(el);
      el->val = mp->fileName;
      slAddHead(&list, el);
      hashAddSaveName(hash, varNameData, el, &el->name);
      // debug
      // fprintf(stderr,"GALT special: saved varNameData:[%s],
      // mp=>fileName:[%s]\n",el->name,el->val);
      // fflush(stderr);
    } else if (mp->multi) {
      warn("unexpected nested MIME structures");
    } else {
      errAbort(
          "mp-> type not data,fileName, or multi - unexpected MIME structure");
    }

    freez(&cdMain);
    freez(&cdName);
    freez(&cdFileName);
  }

  slReverse(&list);
  *retList = list;
  *retHash = hash;
}
#endif /* GBROWSE */

static void parseCookies(struct hash **retHash, struct cgiVar **retList)
/* parses any cookies and puts them into the given hash and list */
{
  char *str;
  char *namePt, *dataPt, *nextNamePt;
  struct hash *hash;
  struct cgiVar *list = NULL, *el;

  /* don't build the hash table again */
  if (haveCookiesHash == TRUE)
    return;

  str = cloneString(getenv("HTTP_COOKIE"));
  if (str == NULL) /* don't have a cookie */
    return;

  hash = newHash(6);

  namePt = str;
  while (isNotEmpty(namePt)) {
    dataPt = strchr(namePt, '=');
    if (dataPt == NULL)
      errAbort("Mangled Cookie input string: no = in '%s' (offset %d in "
               "complete cookie string: '%s')",
               namePt, (int)(namePt - str), getenv("HTTP_COOKIE"));
    *dataPt++ = 0;
    nextNamePt = strchr(dataPt, ';');
    if (nextNamePt != NULL) {
      *nextNamePt++ = 0;
      if (*nextNamePt == ' ')
        nextNamePt++;
    }
    cgiDecode(dataPt, dataPt, strlen(dataPt));
    AllocVar(el);
    el->val = dataPt;
    slAddHead(&list, el);
    hashAddSaveName(hash, namePt, el, &el->name);
    namePt = nextNamePt;
  }

  haveCookiesHash = TRUE;

  slReverse(&list);
  *retList = list;
  *retHash = hash;
}

char *findCookieData(char *varName)
/* Get the string associated with varName from the cookie string. */
{
  struct hashEl *hel;
  char *firstResult;

  /* make sure that the cookie hash table has been created */
  parseCookies(&cookieHash, &cookieList);
  if (cookieHash == NULL)
    return NULL;
  /* Watch out for multiple cookies with the same name (hel is a list) --
   * warn if we find them. */
  hel = hashLookup(cookieHash, varName);
  if (hel == NULL)
    return NULL;
  else
    firstResult = ((struct cgiVar *)hel->val)->val;
  hel = hel->next;
  while (hel != NULL) {
    char *val = ((struct cgiVar *)(hel->val))->val;
    if (sameString(varName, hel->name) && !sameString(firstResult, val)) {
      /* This is too early to call warn -- it will mess up html output. */
      fprintf(stderr, "findCookieData: Duplicate cookie value from IP=%s: "
                      "%s has both %s and %s\n",
              cgiRemoteAddr(), varName, firstResult, val);
    }
    hel = hel->next;
  }
  return firstResult;
}

static char *cgiInputSource(char *s)
/* For NULL sources make a guess as to real source. */
{
  char *qs;
  if (s != NULL)
    return s;
  qs = getenv("QUERY_STRING");
  if (qs == NULL)
    return "POST";
  char *cl = getenv("CONTENT_LENGTH");
  if (cl != NULL && atoi(cl) > 0)
    return "POST";
  return "QUERY";
}

static void _cgiFindInput(char *method)
/* Get raw CGI input into inputString.  Method can be "POST", "QUERY", "GET" or
 * NULL
 * for unknown. */
{
  if (inputString == NULL) {
    method = cgiInputSource(method);
    if (sameWord(method, "POST"))
      getPostInput();
    else if (sameWord(method, "QUERY") || sameWord(method, "GET"))
      getQueryInput();
    else
      errAbort("Unknown form method");
  }
}

static void cgiParseInputAbort(char *input, struct hash **retHash,
                               struct cgiVar **retList)
/* Parse cgi-style input into a hash table and list.  This will alter
 * the input data.  The hash table will contain references back
 * into input, so please don't free input until you're done with
 * the hash. Prints message aborts if there's an error.*/
{
  char *namePt, *dataPt, *nextNamePt;
  struct hash *hash = *retHash;
  struct cgiVar *list = *retList, *el;

  if (!hash)
    hash = newHash(6);
  slReverse(&list);

  namePt = input;
  while (namePt != NULL && namePt[0] != 0) {
    dataPt = strchr(namePt, '=');
    if (dataPt == NULL) {
      errAbort("Mangled CGI input string %s", namePt);
    }
    *dataPt++ = 0;
    nextNamePt = strchr(dataPt, '&');
    if (nextNamePt == NULL)
      nextNamePt = strchr(dataPt, ';'); /* Accomodate DAS. */
    if (nextNamePt != NULL)
      *nextNamePt++ = 0;
    cgiDecode(namePt, namePt, strlen(namePt)); /* for unusual ct names */
    cgiDecode(dataPt, dataPt, strlen(dataPt));
    AllocVar(el);
    el->val = dataPt;
    slAddHead(&list, el);
    hashAddSaveName(hash, namePt, el, &el->name);
    namePt = nextNamePt;
  }
  slReverse(&list);
  *retList = list;
  *retHash = hash;
}

static jmp_buf cgiParseRecover;

static void cgiParseAbort()
/* Abort cgi parsing. */
{
  longjmp(cgiParseRecover, -1);
}

boolean cgiParseInput(char *input, struct hash **retHash,
                      struct cgiVar **retList)
/* Parse cgi-style input into a hash table and list.  This will alter
 * the input data.  The hash table will contain references back
 * into input, so please don't free input until you're done with
 * the hash. Prints message and returns FALSE if there's an error.*/
{
  boolean ok = TRUE;
  int status = setjmp(cgiParseRecover);
  if (status == 0) /* Always true except after long jump. */
  {
    pushAbortHandler(cgiParseAbort);
    cgiParseInputAbort(input, retHash, retList);
  } else /* They long jumped here because of an error. */
  {
    ok = FALSE;
  }
  popAbortHandler();
  return ok;
}

static boolean dumpStackOnSignal = FALSE; // should a stack dump be generated?

static void catchSignal(int sigNum)
/* handler for various terminal signals for logging purposes */
{
  char *sig = NULL;
  switch (sigNum) {
  case SIGABRT:
    sig = "SIGABRT";
    break;
  case SIGSEGV:
    sig = "SIGSEGV";
    break;
  case SIGFPE:
    sig = "SIGFPE";
    break;
  case SIGBUS:
    sig = "SIGBUS";
    break;
  }
  logCgiToStderr();
  fprintf(stderr, "Received signal %s\n", sig);
  if (dumpStackOnSignal)
    dumpStack("Stack for signal %s\n", sig);
  raise(SIGKILL);
}

void initSigHandlers(boolean dumpStack)
/* set handler for various terminal signals for logging purposes.
 * if dumpStack is TRUE, attempt to dump the stack. */
{
  if (cgiIsOnWeb()) {
    signal(SIGABRT, catchSignal);
    signal(SIGSEGV, catchSignal);
    signal(SIGFPE, catchSignal);
    signal(SIGBUS, catchSignal);
    dumpStackOnSignal = dumpStack;
  }
}

static void initCgiInput()
/* Initialize CGI input stuff.  After this CGI vars are
 * stored in an internal hash/list regardless of how they
 * were passed to the program. */
{
  char *s;

  if (inputString != NULL)
    return;

  _cgiFindInput(NULL);

#ifndef GBROWSE
  /* check to see if the input is a multipart form */
  s = getenv("CONTENT_TYPE");
  if (s != NULL && startsWith("multipart/form-data", s)) {
    cgiParseMultipart(&inputHash, &inputList);
  }
#endif /* GBROWSE */

  cgiParseInputAbort(inputString, &inputHash, &inputList);

  /* now parse the cookies */
  parseCookies(&cookieHash, &cookieList);

  /* Set enviroment variables CGIs to enable sql tracing and/or profiling */
  s = cgiOptionalString("JKSQL_TRACE");
  if (s != NULL)
    envUpdate("JKSQL_TRACE", s);
  s = cgiOptionalString("JKSQL_PROF");
  if (s != NULL)
    envUpdate("JKSQL_PROF", s);
}

struct cgiVar *cgiVarList()
/* return the list of cgiVar's */
{
  initCgiInput();
  return inputList;
}

static char *findVarData(char *varName)
/* Get the string associated with varName from the query string. */
{
  struct cgiVar *var;

  initCgiInput();
  if ((var = hashFindVal(inputHash, varName)) == NULL)
    return NULL;
  return var->val;
}

void cgiBadVar(char *varName)
/* Complain about a variable that's not there. */
{
  if (varName == NULL)
    varName = "";
  errAbort("Sorry, didn't find CGI input variable '%s'", varName);
}

static char *mustFindVarData(char *varName)
/* Find variable and associated data or die trying. */
{
  char *res = findVarData(varName);
  if (res == NULL)
    cgiBadVar(varName);
  return res;
}

char *javaScriptLiteralEncode(char *inString)
/* Use backslash escaping on newline
 * and quote chars, backslash and others.
 * Intended that the encoded string will be
 * put between quotes at a higher level and
 * then interpreted by Javascript. */
{
  char c;
  int outSize = 0;
  char *outString, *out, *in;

  if (inString == NULL)
    return (cloneString(""));

  /* Count up how long it will be */
  in = inString;
  while ((c = *in++) != 0) {
    if (c == '\'' || c == '\"' || c == '&' || c == '\\' || c == '\n' ||
        c == '\r' || c == '\t' || c == '\b' || c == '\f')
      outSize += 2;
    else
      outSize += 1;
  }
  outString = needMem(outSize + 1);

  /* Encode string */
  in = inString;
  out = outString;
  while ((c = *in++) != 0) {
    if (c == '\'' || c == '\"' || c == '&' || c == '\\' || c == '\n' ||
        c == '\r' || c == '\t' || c == '\b' || c == '\f')
      *out++ = '\\';
    *out++ = c;
  }
  *out++ = 0;
  return outString;
}

void cgiDecode(char *in, char *out, int inLength)
/* Decode from cgi pluses-for-spaces format to normal.
 * Out will be a little shorter than in typically, and
 * can be the same buffer. */
{
  char c;
  int i;
  for (i = 0; i < inLength; ++i) {
    c = *in++;
    if (c == '+')
      *out++ = ' ';
    else if (c == '%') {
      int code;
      if (sscanf(in, "%2x", &code) != 1)
        code = '?';
      in += 2;
      i += 2;
      *out++ = code;
    } else
      *out++ = c;
  }
  *out++ = 0;
}

char *cgiEncode(char *inString)
/* Return a cgi-encoded version of inString.
 * Alphanumerics kept as is, space translated to plus,
 * and all other characters translated to %hexVal. */
{
  char c;
  int outSize = 0;
  char *outString, *out, *in;

  if (inString == NULL)
    return (cloneString(""));

  /* Count up how long it will be */
  in = inString;
  while ((c = *in++) != 0) {
    if (isalnum(c) || c == ' ' || c == '.' || c == '_')
      outSize += 1;
    else
      outSize += 3;
  }
  outString = needMem(outSize + 1);

  /* Encode string */
  in = inString;
  out = outString;
  while ((c = *in++) != 0) {
    if (isalnum(c) || c == '.' || c == '_')
      *out++ = c;
    else if (c == ' ')
      *out++ = '+';
    else {
      unsigned char uc = c;
      char buf[4];
      *out++ = '%';
      safef(buf, sizeof(buf), "%02X", uc);
      *out++ = buf[0];
      *out++ = buf[1];
    }
  }
  *out++ = 0;
  return outString;
}

char *cgiEncodeFull(char *inString)
/* Return a cgi-encoded version of inString (no + for space!).
 * Alphanumerics/./_ kept as is and all other characters translated to
 * %hexVal. */
{
  char c;
  int outSize = 0;
  char *outString, *out, *in;

  if (inString == NULL)
    return (cloneString(""));

  /* Count up how long it will be */
  in = inString;
  while ((c = *in++) != 0) {
    if (isalnum(c) || c == '.' || c == '_')
      outSize += 1;
    else
      outSize += 3;
  }
  outString = needMem(outSize + 1);

  /* Encode string */
  in = inString;
  out = outString;
  while ((c = *in++) != 0) {
    if (isalnum(c) || c == '.' || c == '_')
      *out++ = c;
    else {
      unsigned char uc = c;
      char buf[4];
      *out++ = '%';
      safef(buf, sizeof(buf), "%02X", uc);
      *out++ = buf[0];
      *out++ = buf[1];
    }
  }
  *out++ = 0;
  return outString;
}

char *cgiOptionalString(char *varName)
/* Return value of string if it exists in cgi environment, else NULL */
{
  return findVarData(varName);
}

char *cgiString(char *varName)
/* Return string value of cgi variable. */
{
  return mustFindVarData(varName);
}

char *cgiUsualString(char *varName, char *usual)
/* Return value of string if it exists in cgi environment.
 * Otherwise return 'usual' */
{
  char *pt;
  pt = findVarData(varName);
  if (pt == NULL)
    pt = usual;
  return pt;
}

struct slName *cgiStringList(char *varName)
/* Find list of cgi variables with given name.  This
 * may be empty.  Free result with slFreeList(). */
{
  struct hashEl *hel;
  struct slName *stringList = NULL, *string;

  initCgiInput();
  for (hel = hashLookup(inputHash, varName); hel != NULL; hel = hel->next) {
    if (sameString(hel->name, varName)) {
      struct cgiVar *var = hel->val;
      string = newSlName(var->val);
      slAddHead(&stringList, string);
    }
  }
  return stringList;
}

int cgiInt(char *varName)
/* Return int value of cgi variable. */
{
  char *data;
  char c;

  data = mustFindVarData(varName);
  data = skipLeadingSpaces(data);
  c = data[0];
  if (!(isdigit(c) || (c == '-' && isdigit(data[1]))))
    errAbort("Expecting number in %s, got \"%s\"\n", varName, data);
  return atoi(data);
}

int cgiIntExp(char *varName)
/* Evaluate an integer expression in varName and
 * return value. */
{
  return intExp(cgiString(varName));
}

int cgiOptionalInt(char *varName, int defaultVal)
/* This returns integer value of varName if it exists in cgi environment
 * and it's not just the empty string otherwise it returns defaultVal. */
{
  char *s = cgiOptionalString(varName);
  s = skipLeadingSpaces(s);
  if (isEmpty(s))
    return defaultVal;
  return cgiInt(varName);
}

double cgiDouble(char *varName)
/* Returns double value. */
{
  char *data;
  double x;

  data = mustFindVarData(varName);
  if (sscanf(data, "%lf", &x) < 1)
    errAbort("Expecting real number in %s, got \"%s\"\n", varName, data);
  return x;
}

double cgiOptionalDouble(char *varName, double defaultVal)
/* Returns double value. */
{
  if (!cgiVarExists(varName))
    return defaultVal;
  return cgiDouble(varName);
}

boolean cgiVarExists(char *varName)
/* Returns TRUE if the variable was passed in. */
{
  initCgiInput();
  return hashLookup(inputHash, varName) != NULL;
}

boolean cgiBoolean(char *varName) { return cgiVarExists(varName); }

int cgiOneChoice(char *varName, struct cgiChoice *choices, int choiceSize)
/* Returns value associated with string variable in choice table. */
{
  char *key = cgiString(varName);
  int i;
  int val = -1;

  for (i = 0; i < choiceSize; ++i) {
    if (sameWord(choices[i].name, key)) {
      val = choices[i].value;
      return val;
    }
  }
  errAbort("Unknown key %s for variable %s\n", key, varName);
  return val;
}

void cgiMakeSubmitButton()
/* Make 'submit' type button. */
{
  cgiMakeButton("Submit", "Submit");
}

void cgiMakeResetButton()
/* Make 'reset' type button. */
{
  printf("<INPUT TYPE=RESET NAME=\"Reset\" VALUE=\" Reset \">");
}

void cgiMakeClearButton(char *form, char *field)
/* Make button to clear a text field. */
{
  char javascript[1024];

  safef(javascript, sizeof(javascript),
        "document.%s.%s.value = ''; document.%s.submit();", form, field, form);
  cgiMakeOnClickButton(javascript, " Clear  ");
}

void cgiMakeButtonWithMsg(char *name, char *value, char *msg)
/* Make 'submit' type button. Display msg on mouseover, if present*/
{
  printf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" %s%s%s>", name, value,
         (msg ? " TITLE=\"" : ""), (msg ? msg : ""), (msg ? "\"" : ""));
}

void cgiMakeButtonWithOnClick(char *name, char *value, char *msg, char *onClick)
/* Make 'submit' type button, with onclick javascript */
{
  printf(
      "<input type=\"submit\" name=\"%s\" value=\"%s\" onclick=\"%s\" %s%s%s>",
      name, value, onClick, (msg ? " TITLE=\"" : ""), (msg ? msg : ""),
      (msg ? "\"" : ""));
}

void cgiMakeButton(char *name, char *value)
/* Make 'submit' type button */
{
  cgiMakeButtonWithMsg(name, value, NULL);
}

void cgiMakeOnClickButton(char *command, char *value)
/* Make 'push' type button with client side onClick (java)script. */
{
  printf("<INPUT TYPE=\"button\" VALUE=\"%s\" onClick=\"%s\">", value, command);
}

void cgiMakeOnClickSubmitButton(char *command, char *name, char *value)
/* Make submit button with both variable name and value with client side
 * onClick (java)script. */
{
  printf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" onClick=\"%s\">", name,
         value, command);
}

void cgiMakeOptionalButton(char *name, char *value, boolean disabled)
/* Make 'submit' type button that can be disabled. */
{
  printf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\"", name, value);
  if (disabled)
    printf(" DISABLED");
  printf(">");
}

void cgiMakeFileEntry(char *name)
/* Make file entry box/browser */
{
  printf("<INPUT TYPE=FILE NAME=\"%s\">", name);
}

void cgiSimpleTableStart()
/* start HTML table  -- no customization. Leaves room
 * for a fancier implementation */
{
  printf("<TABLE>\n");
}

void cgiTableEnd()
/* end HTML table */
{
  printf("</TABLE>\n");
}

void cgiSimpleTableRowStart()
/* Start table row */
{
  printf("<TR>\n");
}

void cgiTableRowEnd()
/* End table row */
{
  printf("</TR>\n");
}

void cgiSimpleTableFieldStart()
/* Start table field */
{
  printf("<TD>");
}

void cgiTableFieldStartAlignRight()
/* Start table field and align right*/
{
  printf("<TD ALIGN = RIGHT>");
}

void cgiTableFieldEnd()
/* End table field */
{
  printf("</TD>\n");
}

void cgiTableField(char *text)
/* Make table field entry */
{
  printf("<TD> %s </TD>\n", text);
}

void cgiTableFieldWithMsg(char *text, char *msg)
/* Make table field entry with mouseover */
{
  printf("<TD %s%s%s> %s </TD>\n", (msg ? " TITLE=\"" : ""), (msg ? msg : ""),
         (msg ? "\"" : ""), text);
}

void cgiParagraph(char *text)
/* Make text paragraph */
{
  printf("<P> %s\n", text);
}

void cgiMakeRadioButton(char *name, char *value, boolean checked)
/* Make radio type button.  A group of radio buttons should have the
 * same name but different values.   The default selection should be
 * sent with checked on. */
{
  printf("<INPUT TYPE=RADIO NAME=\"%s\" VALUE=\"%s\" %s>", name, value,
         (checked ? "CHECKED" : ""));
}

void cgiMakeOnClickRadioButton(char *name, char *value, boolean checked,
                               char *command)
/* Make radio type button with onClick command.
 *  A group of radio buttons should have the
 * same name but different values.   The default selection should be
 * sent with checked on. */
{
  printf("<INPUT TYPE=RADIO NAME=\"%s\" VALUE=\"%s\" %s %s>", name, value,
         command, (checked ? "CHECKED" : ""));
}

char *cgiBooleanShadowPrefix()
/* Prefix for shadow variable set with boolean variables. */
{
  return "boolshad.";
}
#define BOOLSHAD_EXTRA "class='cbShadow'"

boolean cgiBooleanDefined(char *name)
/* Return TRUE if boolean variable is defined (by
 * checking for shadow. */
{
  char buf[256];
  safef(buf, sizeof(buf), "%s%s", cgiBooleanShadowPrefix(), name);
  return cgiVarExists(buf);
}

static void cgiMakeCheckBox2Bool(char *name, boolean checked, boolean enabled,
                                 char *id, char *moreHtml)
/* Make check box - designed to be called by the variously overloaded
 * cgiMakeCheckBox functions, and should NOT be called directly.
 * moreHtml: optional additional html like javascript call or mouseover msg (may
 * be NULL)
 * id: button id (may be NULL)
 * Also make a shadow hidden variable and support 2 boolean states:
 *    checked/unchecked and enabled/disabled. */
{
  char buf[256], idBuf[256];

  if (id)
    safef(idBuf, sizeof(idBuf), " id=\"%s\"", id);
  else
    idBuf[0] = 0;

  printf("<INPUT TYPE=CHECKBOX NAME=\"%s\"%s VALUE=on %s%s%s>", name, idBuf,
         (moreHtml ? moreHtml : ""), (checked ? " CHECKED" : ""),
         (enabled ? "" : " DISABLED"));
  safef(buf, sizeof(buf), "%s%s", cgiBooleanShadowPrefix(), name);
  cgiMakeHiddenVarWithExtra(buf, (enabled ? "0" : (checked ? "-1" : "-2")),
                            BOOLSHAD_EXTRA);
}

void cgiMakeCheckBoxUtil(char *name, boolean checked, char *msg, char *id)
/* Make check box - can be called directly, though it was originally meant
 * as the common code for all lower level checkbox routines.
 * However, it's util functionality has been taken over by
 * cgiMakeCheckBoxWithIdAndOptionalHtml() */
{
  char buf[256];

  if (msg)
    safef(buf, sizeof(buf), "TITLE=\"%s\"", msg);
  else
    buf[0] = 0;

  cgiMakeCheckBox2Bool(name, checked, TRUE, id, buf);
}

void cgiMakeCheckBoxWithMsg(char *name, boolean checked, char *msg) {
  char buf[512];
  safef(buf, sizeof(buf), "title='%s'", msg);
  cgiMakeCheckBox2Bool(name, checked, TRUE, NULL, buf);
}

void cgiMakeCheckBoxWithId(char *name, boolean checked, char *id)
/* Make check box, which includes an ID. */
{
  cgiMakeCheckBox2Bool(name, checked, TRUE, id, NULL);
}

void cgiMakeCheckBox(char *name, boolean checked)
/* Make check box. */
{
  cgiMakeCheckBox2Bool(name, checked, TRUE, NULL, NULL);
}

void cgiMakeCheckBoxJS(char *name, boolean checked, char *javascript)
/* Make check box with javascript. */
{
  cgiMakeCheckBox2Bool(name, checked, TRUE, NULL, javascript);
}

void cgiMakeCheckBoxIdAndJS(char *name, boolean checked, char *id,
                            char *javascript)
/* Make check box with ID and javascript. */
{
  cgiMakeCheckBox2Bool(name, checked, TRUE, id, javascript);
}

void cgiMakeCheckBoxFourWay(char *name, boolean checked, boolean enabled,
                            char *id, char *classes, char *moreHtml)
/* Make check box - with fourWay functionality (checked/unchecked by
 * enabled/disabled)
 * Also makes a shadow hidden variable that supports the 2 boolean states. */
{
  char shadName[256];

  printf("<INPUT TYPE=CHECKBOX NAME='%s'", name);
  if (id)
    printf(" id='%s'", id);
  if (checked)
    printf(" CHECKED");
  if (!enabled) {
    if (findWordByDelimiter("disabled", ' ', classes) == NULL) // fauxDisabled ?
      printf(" DISABLED");
  }
  if (classes)
    printf(" class='%s'", classes);
  if (moreHtml)
    printf(" %s", moreHtml);
  printf(">");

  // The hidden var needs to hold the 4way state
  safef(shadName, sizeof(shadName), "%s%s", cgiBooleanShadowPrefix(), name);
  cgiMakeHiddenVarWithExtra(shadName, (enabled ? "0" : (checked ? "-1" : "-2")),
                            BOOLSHAD_EXTRA);
}

void cgiMakeHiddenBoolean(char *name, boolean on)
/* Make hidden boolean variable. Also make a shadow hidden variable so we
 * can distinguish between variable not present and
 * variable set to false. */
{
  char buf[256];
  cgiMakeHiddenVar(name, on ? "on" : "off");
  safef(buf, sizeof(buf), "%s%s", cgiBooleanShadowPrefix(), name);
  cgiMakeHiddenVarWithExtra(buf, "1", BOOLSHAD_EXTRA);
}

void cgiMakeTextArea(char *varName, char *initialVal, int rowCount,
                     int columnCount)
/* Make a text area with area rowCount X columnCount and with text: intialVal */
{
  cgiMakeTextAreaDisableable(varName, initialVal, rowCount, columnCount, FALSE);
}

void cgiMakeTextAreaDisableable(char *varName, char *initialVal, int rowCount,
                                int columnCount, boolean disabled)
/* Make a text area that can be disabled. The rea has rowCount X
 * columnCount and with text: intialVal */
{
  printf("<TEXTAREA NAME=\"%s\" ROWS=%d COLS=%d %s>%s</TEXTAREA>", varName,
         rowCount, columnCount, disabled ? "DISABLED" : "",
         (initialVal != NULL ? initialVal : ""));
}

void cgiMakeOnKeypressTextVar(char *varName, char *initialVal, int charSize,
                              char *script)
/* Make a text control filled with initial value, with a (java)script
 * to execute every time a key is pressed.  If charSize is zero it's
 * calculated from initialVal size. */
{
  if (initialVal == NULL)
    initialVal = "";
  if (charSize == 0)
    charSize = strlen(initialVal);
  if (charSize == 0)
    charSize = 8;

  printf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=%d VALUE=\"%s\"", varName, charSize,
         initialVal);
  if (isNotEmpty(script))
    printf(" onkeypress=\"%s\"", script);
  printf(">\n");
}

void cgiMakeTextVar(char *varName, char *initialVal, int charSize)
/* Make a text control filled with initial value.  If charSize
 * is zero it's calculated from initialVal size. */
{
  cgiMakeOnKeypressTextVar(varName, initialVal, charSize, NULL);
}

void cgiMakeTextVarWithExtraHtml(char *varName, char *initialVal, int width,
                                 char *extra)
/* Make a text control filled with initial value. */
{
  if (initialVal == NULL)
    initialVal = "";
  if (width == 0)
    width = strlen(initialVal) * 10;
  if (width == 0)
    width = 100;

  printf("<INPUT TYPE=TEXT class='inputBox' NAME=\"%s\" style='width: %dpx' "
         "VALUE=\"%s\"",
         varName, width, initialVal);
  if (isNotEmpty(extra))
    printf(" %s", extra);
  printf(">\n");
}

void cgiMakeIntVar(char *varName, int initialVal, int maxDigits)
/* Make a text control filled with initial value.  */
{
  if (maxDigits == 0)
    maxDigits = 4;

  printf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=%d VALUE=%d>", varName, maxDigits,
         initialVal);
}

void cgiMakeIntVarInRange(char *varName, int initialVal, char *title, int width,
                          char *min, char *max)
/* Make a integer control filled with initial value.
   If min and/or max are non-NULL will enforce range
   Requires utils.js jQuery.js and inputBox class */
{
  if (width == 0) {
    if (max)
      width = strlen(max) * 10;
    else {
      int sz = initialVal + 1000;
      if (min)
        sz = atoi(min) + 1000;
      width = 10;
      while (sz /= 10)
        width += 10;
    }
  }
  if (width < 65)
    width = 65;

  printf("<INPUT TYPE=TEXT class='inputBox' name=\"%s\" style='width: %dpx' "
         "value=%d",
         varName, width, initialVal);
  printf(" onChange='return validateInt(this,%s,%s);'",
         (min ? min : "\"null\""), (max ? max : "\"null\""));
  if (title)
    printf(" title='%s'", title);
  printf(">\n");
}

void cgiMakeIntVarWithLimits(char *varName, int initialVal, char *title,
                             int width, int min, int max) {
  char minLimit[20];
  char maxLimit[20];
  char *minStr = NULL;
  char *maxStr = NULL;
  if (min != NO_VALUE) {
    safef(minLimit, sizeof(minLimit), "%d", min);
    minStr = minLimit;
  }
  if (max != NO_VALUE) {
    safef(maxLimit, sizeof(maxLimit), "%d", max);
    maxStr = maxLimit;
  }
  cgiMakeIntVarInRange(varName, initialVal, title, width, minStr, maxStr);
}

void cgiMakeIntVarWithMin(char *varName, int initialVal, char *title, int width,
                          int min) {
  char minLimit[20];
  char *minStr = NULL;
  if (min != NO_VALUE) {
    safef(minLimit, sizeof(minLimit), "%d", min);
    minStr = minLimit;
  }
  cgiMakeIntVarInRange(varName, initialVal, title, width, minStr, NULL);
}

void cgiMakeIntVarWithMax(char *varName, int initialVal, char *title, int width,
                          int max) {
  char maxLimit[20];
  char *maxStr = NULL;
  if (max != NO_VALUE) {
    safef(maxLimit, sizeof(maxLimit), "%d", max);
    maxStr = maxLimit;
  }
  cgiMakeIntVarInRange(varName, initialVal, title, width, NULL, maxStr);
}

void cgiMakeDoubleVar(char *varName, double initialVal, int maxDigits)
/* Make a text control filled with initial floating-point value.  */
{
  if (maxDigits == 0)
    maxDigits = 4;

  printf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=%d VALUE=%g>", varName, maxDigits,
         initialVal);
}

void cgiMakeDoubleVarInRange(char *varName, double initialVal, char *title,
                             int width, char *min, char *max)
/* Make a floating point control filled with initial value.
   If min and/or max are non-NULL will enforce range
   Requires utils.js jQuery.js and inputBox class */
{
  if (width == 0) {
    if (max)
      width = strlen(max) * 10;
  }
  if (width < 65)
    width = 65;

  printf("<INPUT TYPE=TEXT class='inputBox' name=\"%s\" style='width: %dpx' "
         "value=%g",
         varName, width, initialVal);
  printf(" onChange='return validateFloat(this,%s,%s);'",
         (min ? min : "\"null\""), (max ? max : "\"null\""));
  if (title)
    printf(" title='%s'", title);
  printf(">\n");
}

void cgiMakeDoubleVarWithLimits(char *varName, double initialVal, char *title,
                                int width, double min, double max) {
  char minLimit[20];
  char maxLimit[20];
  char *minStr = NULL;
  char *maxStr = NULL;
  if ((int)min != NO_VALUE) {
    safef(minLimit, sizeof(minLimit), "%g", min);
    minStr = minLimit;
  }
  if ((int)max != NO_VALUE) {
    safef(maxLimit, sizeof(maxLimit), "%g", max);
    maxStr = maxLimit;
  }
  cgiMakeDoubleVarInRange(varName, initialVal, title, width, minStr, maxStr);
}

void cgiMakeDoubleVarWithMin(char *varName, double initialVal, char *title,
                             int width, double min) {
  char minLimit[20];
  char *minStr = NULL;
  if ((int)min != NO_VALUE) {
    safef(minLimit, sizeof(minLimit), "%g", min);
    minStr = minLimit;
  }
  cgiMakeDoubleVarInRange(varName, initialVal, title, width, minStr, NULL);
}

void cgiMakeDoubleVarWithMax(char *varName, double initialVal, char *title,
                             int width, double max) {
  char maxLimit[20];
  char *maxStr = NULL;
  if ((int)max != NO_VALUE) {
    safef(maxLimit, sizeof(maxLimit), "%g", max);
    maxStr = maxLimit;
  }
  cgiMakeDoubleVarInRange(varName, initialVal, title, width, NULL, maxStr);
}

void cgiMakeDropListClassWithStyleAndJavascript(char *name, char *menu[],
                                                int menuSize, char *checked,
                                                char *class, char *style,
                                                char *javascript)
/* Make a drop-down list with names, text class, style and javascript. */
{
  int i;
  char *selString;
  if (checked == NULL)
    checked = menu[0];
  printf("<SELECT");
  if (name)
    printf(" NAME='%s'", name);
  if (class)
    printf(" class='%s'", class);
  if (style)
    printf(" style='%s'", style);
  if (javascript)
    printf(" %s", javascript);
  printf(">\n");
  for (i = 0; i < menuSize; ++i) {
    if (sameWord(menu[i], checked))
      selString = " SELECTED";
    else
      selString = "";
    printf("<OPTION%s>%s</OPTION>\n", selString, menu[i]);
  }
  printf("</SELECT>\n");
}

void cgiMakeDropListClassWithStyle(char *name, char *menu[], int menuSize,
                                   char *checked, char *class, char *style)
/* Make a drop-down list with names, text class and style. */
{
  cgiMakeDropListClassWithStyleAndJavascript(name, menu, menuSize, checked,
                                             class, style, "");
}

void cgiMakeDropListClass(char *name, char *menu[], int menuSize, char *checked,
                          char *class)
/* Make a drop-down list with names. */
{
  cgiMakeDropListClassWithStyle(name, menu, menuSize, checked, class, NULL);
}

void cgiMakeDropList(char *name, char *menu[], int menuSize, char *checked)
/* Make a drop-down list with names.
 * uses style "normalText" */
{
  cgiMakeDropListClass(name, menu, menuSize, checked, "normalText");
}

char *cgiMultListShadowPrefix()
/* Prefix for shadow variable set with multi-select inputs. */
{
  return "multishad.";
}

void cgiMakeMultList(char *name, char *menu[], int menuSize,
                     struct slName *checked, int length)
/* Make a list of names with window height equalt to length,
 * which can have multiple selections. Same as drop-down list
 * except "multiple" is added to select tag. */
{
  int i;
  char *selString;
  if (checked == NULL)
    checked = slNameNew(menu[0]);
  printf("<SELECT MULTIPLE SIZE=%d ALIGN=CENTER NAME=\"%s\">\n", length, name);
  for (i = 0; i < menuSize; ++i) {
    if (slNameInList(checked, menu[i]))
      selString = " SELECTED";
    else
      selString = "";
    printf("<OPTION%s>%s</OPTION>\n", selString, menu[i]);
  }
  printf("</SELECT>\n");
  char buf[512];
  safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
  cgiMakeHiddenVar(buf, "1");
}

void cgiMakeCheckboxGroupWithVals(char *name, char *menu[], char *values[],
                                  int menuSize, struct slName *checked,
                                  int tableColumns)
/* Make a table of checkboxes that have the same variable name but different
 * values (same behavior as a multi-select input), with nice labels in menu[].
 */
{
  int i;
  if (values == NULL)
    values = menu;
  if (menu == NULL)
    menu = values;
  puts("<TABLE BORDERWIDTH=0><TR>");
  for (i = 0; i < menuSize; i++) {
    if (i > 0 && (i % tableColumns) == 0)
      printf("</TR><TR>");
    printf("<TD><INPUT TYPE=CHECKBOX NAME=\"%s\" VALUE=\"%s\" %s> %s</TD>\n",
           name, values[i], (slNameInList(checked, values[i]) ? "CHECKED" : ""),
           menu[i]);
  }
  if ((i % tableColumns) != 0)
    while ((i++ % tableColumns) != 0)
      printf("<TD></TD>");
  puts("</TR></TABLE>");
  char buf[512];
  safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
  cgiMakeHiddenVar(buf, "0");
}

void cgiMakeCheckboxGroup(char *name, char *menu[], int menuSize,
                          struct slName *checked, int tableColumns)
/* Make a table of checkboxes that have the same variable name but different
 * values (same behavior as a multi-select input). */
{
  cgiMakeCheckboxGroupWithVals(name, menu, NULL, menuSize, checked,
                               tableColumns);
}

void cgiMakeDropListFull(char *name, char *menu[], char *values[], int menuSize,
                         char *checked, char *extraAttribs)
/* Make a drop-down list with names and values. */
{
  int i;
  char *selString;
  if (checked == NULL)
    checked = menu[0];

  if (NULL != extraAttribs) {
    printf("<SELECT NAME=\"%s\" %s>\n", name, extraAttribs);
  } else {
    printf("<SELECT NAME=\"%s\">\n", name);
  }

  for (i = 0; i < menuSize; ++i) {
    if (sameWord(values[i], checked))
      selString = " SELECTED";
    else
      selString = "";
    printf("<OPTION%s VALUE=\"%s\">%s</OPTION>\n", selString, values[i],
           menu[i]);
  }
  printf("</SELECT>\n");
}

char *cgiMakeSelectDropList(boolean multiple, char *name,
                            struct slPair *valsAndLabels, char *selected,
                            char *anyAll, char *extraClasses, char *extraHtml)
// Returns allocated string of HTML defining a drop-down select
// (if multiple, REQUIRES ui-dropdownchecklist.js)
// valsAndLabels: val (pair->name) must be filled in but label (pair->val) may
// be NULL.
// selected: if not NULL is a val found in the valsAndLabels (multiple then
// comma delimited list).
//           If null and anyAll not NULL, that will be selected
// anyAll: if not NULL is the string for an initial option. It can contain val
// and label,
//         delimited by a comma
// extraHtml: if not NULL contains id, javascript calls and style.
//            It does NOT contain class definitions
{
  struct dyString *output = dyStringNew(1024);
  boolean checked = FALSE;

  dyStringPrintf(output, "<SELECT name='%s'", name);
  if (multiple)
    dyStringAppend(output, " MULTIPLE");
  if (extraClasses != NULL)
    dyStringPrintf(output, " class='%s%s'", extraClasses,
                   (multiple ? " filterBy" : ""));
  else if (multiple)
    dyStringAppend(output, " class='filterBy'");

  if (extraHtml != NULL)
    dyStringPrintf(output, " %s", extraHtml);
  dyStringAppend(output, ">\n");

  // Handle initial option "Any" or "All"
  if (anyAll != NULL) {
    char *val = anyAll;             // Could contain a label after the value
    char *label = strchr(val, ','); // Could contain a label after the value
    if (label != NULL) {
      val = cloneString(anyAll);
      label = strchr(val, ','); // again because this is new mem
      *label = '\0';
      label = label + 1;
    } else
      label = val;
    checked = TRUE; // The default case
    if (selected != NULL) {
      if (multiple)
        checked = (findWordByDelimiter(val, ',', selected) != NULL);
      else
        checked = sameString(val, selected);
    }
    dyStringPrintf(output, "<OPTION%s VALUE='%s'>%s</OPTION>\n",
                   (checked ? " SELECTED" : ""), val,
                   javaScriptLiteralEncode(label));
    if (label != val)
      freeMem(val);
  }

  // All other options
  struct slPair *valPair = valsAndLabels;
  for (; valPair != NULL; valPair = valPair->next) {
    checked = FALSE;
    if (selected != NULL) {
      if (multiple)
        checked = (findWordByDelimiter(valPair->name, ',', selected) != NULL);
      else
        checked = sameString(valPair->name, selected);
    }
    char *label = valPair->name;
    if (valPair->val != NULL)
      label = valPair->val;
    dyStringPrintf(output, "<OPTION%s VALUE='%s'>%s</OPTION>\n",
                   (checked ? " SELECTED" : ""), (char *)valPair->name,
                   javaScriptLiteralEncode(label));
  }

  dyStringPrintf(output, "</SELECT>\n");

  return dyStringCannibalize(&output);
}

void cgiMakeDropListWithVals(char *name, char *menu[], char *values[],
                             int menuSize, char *checked)
/* Make a drop-down list with names and values. In this case checked
 * corresponds to a value, not a menu. */
{
  int i;
  char *selString;
  if (checked == NULL)
    checked = values[0];

  printf("<SELECT NAME=\"%s\">\n", name);
  for (i = 0; i < menuSize; ++i) {
    if (sameWord(values[i], checked))
      selString = " SELECTED";
    else
      selString = "";
    printf("<OPTION%s VALUE=\"%s\">%s</OPTION>\n", selString, values[i],
           menu[i]);
  }
  printf("</SELECT>\n");
}

void cgiDropDownWithTextValsAndExtra(char *name, char *text[], char *values[],
                                     int count, char *selected, char *extra)
/* Make a drop-down list with both text and values. */
{
  int i;
  char *selString;
  assert(values != NULL && text != NULL);
  if (selected == NULL)
    selected = values[0];
  printf("<SELECT");
  if (name)
    printf(" NAME='%s'", name);
  if (extra)
    printf("%s", extra);
  printf(">\n");
  for (i = 0; i < count; ++i) {
    if (sameWord(values[i], selected))
      selString = " SELECTED";
    else
      selString = "";
    printf("<OPTION%s value='%s'>%s</OPTION>\n", selString, values[i], text[i]);
  }
  printf("</SELECT>\n");
}

void cgiMakeHiddenVarWithExtra(char *varName, char *string, char *extra)
/* Store string in hidden input for next time around. */
{
  printf("<INPUT TYPE=HIDDEN NAME='%s' VALUE='%s'", varName, string);
  if (extra)
    printf(" %s>\n", extra);
  else
    puts(">");
}

void cgiContinueHiddenVar(char *varName)
/* Write CGI var back to hidden input for next time around. */
{
  if (cgiVarExists(varName))
    cgiMakeHiddenVar(varName, cgiString(varName));
}

void cgiVarExclude(char *varName)
/* If varName exists, remove it. */
{
  if (cgiVarExists(varName)) {
    struct cgiVar *cv = hashRemove(inputHash, varName);
    slRemoveEl(&inputList, cv);
  }
}

void cgiVarExcludeExcept(char **varNames)
/* Exclude all variables except for those in NULL
 * terminated array varNames.  varNames may be NULL
 * in which case nothing is excluded. */
{
  struct hashEl *list, *el;
  struct hash *exclude = newHash(8);
  char *s;

  /* Build up hash of things to exclude */
  if (varNames != NULL) {
    while ((s = *varNames++) != NULL)
      hashAdd(exclude, s, NULL);
  }

  /* Step through variable list and remove them if not
   * excluded. */
  initCgiInput();
  list = hashElListHash(inputHash);
  for (el = list; el != NULL; el = el->next) {
    if (!hashLookup(exclude, el->name))
      cgiVarExclude(el->name);
  }
  hashElFreeList(&list);
  freeHash(&exclude);
}

void cgiVarSet(char *varName, char *val)
/* Set a cgi variable to a particular value. */
{
  struct cgiVar *var;
  initCgiInput();
  AllocVar(var);
  var->val = cloneString(val);
  hashAddSaveName(inputHash, varName, var, &var->name);
}

struct dyString *cgiUrlString()
/* Get URL-formatted that expresses current CGI variable state. */
{
  struct dyString *dy = newDyString(0);
  struct cgiVar *cv;
  char *e;

  for (cv = inputList; cv != NULL; cv = cv->next) {
    if (cv != inputList)
      dyStringAppend(dy, "&");
    e = cgiEncode(cv->val);
    dyStringPrintf(dy, "%s=", cv->name);
    dyStringAppend(dy, e);
    freez(&e);
  }
  return dy;
}

void cgiContinueAllVars()
/* Write back all CGI vars as hidden input for next time around. */
{
  struct cgiVar *cv;
  for (cv = inputList; cv != NULL; cv = cv->next)
    cgiMakeHiddenVar(cv->name, cv->val);
}

boolean cgiFromCommandLine(int *pArgc, char *argv[], boolean preferWeb)
/* Use the command line to set up things as if we were a CGI program.
 * User types in command line (assuming your program called cgiScript)
 * like:
 *        cgiScript nonCgiArg1 var1=value1 var2=value2 var3=value3 nonCgiArg2
 * or like
 *        cgiScript nonCgiArg1 var1=value1&var2=value2&var3=value3 nonCgiArg2
 * or even like
 *        cgiScript nonCgiArg1 -x -y=bogus z=really
 * (The non-cgi arguments can occur anywhere.  The cgi arguments (all containing
 * the character '=' or starting with '-') are erased from argc/argv.  Normally
 * you call this cgiSpoof(&argc, argv);
 */
{
  int argc = *pArgc;
  int i;
  int argcLeft = argc;
  char *name;
  static char queryString[16384];
  char *q = queryString;
  boolean needAnd = TRUE;
  boolean gotAny = FALSE;
  boolean startDash;
  boolean gotEq;
  static char hostLine[512];

  if (preferWeb && cgiIsOnWeb())
    return TRUE; /* No spoofing required! */
  q += safef(q, queryString + sizeof(queryString) - q, "%s",
             "QUERY_STRING=cgiSpoof=on");
  for (i = 0; i < argcLeft;) {
    name = argv[i];
    if ((startDash = (name[0] == '-')))
      ++name;
    gotEq = (strchr(name, '=') != NULL);
    if (gotEq || startDash) {
      if (needAnd)
        *q++ = '&';
      q += safef(q, queryString + sizeof(queryString) - q, "%s", name);
      if (!gotEq || strchr(name, '&') == NULL)
        needAnd = TRUE;
      if (!gotEq)
        q += safef(q, queryString + sizeof(queryString) - q, "=on");
      memcpy(&argv[i], &argv[i + 1], sizeof(argv[i]) * (argcLeft - i - 1));
      argcLeft -= 1;
      gotAny = TRUE;
    } else
      i++;
  }
  if (gotAny) {
    *pArgc = argcLeft;
  }
  putenv("REQUEST_METHOD=GET");
  putenv(queryString);
  char *host = getenv("HOST");
  if (host == NULL)
    host = "unknown";
  safef(hostLine, sizeof(hostLine), "SERVER_NAME=%s", host);
  putenv(hostLine);
  initCgiInput();
  return gotAny;
}

boolean cgiSpoof(int *pArgc, char *argv[])
/* If run from web line set up input
 * variables from web line, otherwise
 * set up from command line. */
{
  return cgiFromCommandLine(pArgc, argv, TRUE);
}

boolean cgiFromFile(char *fileName)
/* Set up a cgi environment using parameters stored in a file.
 * Takes file with arguments in the form:
 *       argument1=someVal
 *       # This is a comment
 *       argument2=someOtherVal
 *       ...
 * and puts them into the cgi environment so that the usual
 * cgiGetVar() commands can be used. Useful when a program
 * has a lot of possible parameters.
 */
{
  char **argv = NULL;
  int argc = 0;
  int maxArgc = 10;
  int i;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *line;
  boolean spoof = FALSE;
  AllocArray(argv, maxArgc);
  /* Remember that first arg is program name.
     Put filename there instead. */
  argc = 1;
  argv[0] = cloneString(fileName);
  for (;;) {
    /* If we are at the end we're done. */
    if (!lineFileNext(lf, &line, NULL))
      break;
    /* If it is a comment or blank line skip it. */
    if (line[0] == '#' || sameString(line, ""))
      continue;
    /* If our argv array is full expand it. */
    if ((argc + 1) >= maxArgc) {
      ExpandArray(argv, maxArgc, 2 * maxArgc);
      maxArgc *= 2;
    }
    /* Fill in another argument to our psuedo arguments. */
    argv[argc++] = cloneString(line);
  }
  spoof = cgiSpoof(&argc, argv);
  /* Cleanup. */
  lineFileClose(&lf);
  for (i = 0; i < argc; i++)
    freez(&argv[i]);
  freez(&argv);
  return spoof;
}

void logCgiToStderr()
/* Log useful CGI info to stderr */
{
  char *ip = getenv("REMOTE_ADDR");
  char *cgiBinary = getenv("SCRIPT_FILENAME");
  char *requestUri = getenv("REQUEST_URI");
  char *hgsid = cgiOptionalString("hgsid");
  char *cgiFileName = NULL;
  time_t nowTime = time(NULL);
  struct tm *tm;
  tm = localtime(&nowTime);
  char *ascTime = asctime(tm);
  size_t len = strlen(ascTime);
  if (cgiBinary)
    cgiFileName = basename(cgiBinary);
  else
    cgiFileName = "cgi-bin";
  if (len > 3)
    ascTime[len - 2] = '\0';
  if (!ip)
    ip = "unknown";
  if (!hgsid)
    hgsid = "unknown";
  if (!requestUri)
    requestUri = "unknown";
  fprintf(stderr, "[%s] [%s] [client %s] [hgsid=%.24s] [%.1024s] ", ascTime,
          cgiFileName, ip, hgsid, requestUri);
}

void cgiResetState()
/* This is for reloading CGI settings multiple times in the same program
 * execution.  No effect if state has not yet been initialized. */
{
  freez(&inputString);
  inputString = NULL;
  if (inputHash != NULL)
    hashFree(&inputHash);
  inputHash = NULL;
  inputList = NULL;

  haveCookiesHash = FALSE;
  if (cookieHash != NULL)
    hashFree(&cookieHash);
  cookieHash = NULL;
  cookieList = NULL;
}

void cgiDown(float lines)
// Drop down a certain number of lines (may be fractional)
{
  printf("<div style='height:%fem;'></div>\n", lines);
}

char *commonCssStyles()
/* Returns a string of common CSS styles */
{
  // Contents currently is OBSOLETE as these have been moved to HGStyle.css
  // TODO: remove all traces (from web.c, hgTracks, hgTables) as this funtion
  // does nothing.
  return "";
}
